The Role Of Microorganisms In Coffee Fermentation: The two main phenomena that occur during the post-harvest processing of coffee (collectively referred to as fermentation) are microbial activity in the processing environment and the metabolism of substances within the beans.
The kinetics of fermentation focuses on the consumption of nutrients (of the coffee cherries) and the generation of microbial secondary metabolites, as well as the continuous transformation of flavor substances in the bean (i.e. variation in the composition, and proportions of various compounds in the coffee bean).
This complexity comes from the many stages of a processing process as well as the dependence on other external factors such as temperature, coffee variety, processing equipment, etc.
Actually, the full title of this article is The Role of Microbial and Intracellular Metabolism in Coffee Fermentation Processes and Impact on Flavor Potential– However much of the article’s content focuses on the impact of bacteria on wet processing, I shortened the title of the article to make it simpler.
Microbiology & Coffee Fermentation
Microorganisms are present in almost every environment and therefore in the coffee processing cycle, they play an important role as they do in other fermented food products. Microorganisms are always present on the coffee bean surface even before processing begins: as processing takes place, these microorganisms (especially lactic acid bacteria) grow based on nutrient-rich plant materials, such as pods or mucilage, that are completely released into the environment.
Microorganisms are ubiquitous in the various stages of post-harvest coffee processing, including acetic acid bacteria, lactic acid bacteria, bacilli, yeasts, and filamentous fungi. It is clear to what extent microorganisms are required to produce high-quality coffee.
During growth, microorganisms produce metabolites from the phytonutrient source and accumulate in the processing medium – This is known as fermentation by the microbiota.
In wet processing, fermentation of the coffee occurs in the maceration tank, while with dry processing, fermentation occurs in the cherries’ outer layers. However, some metabolites produced during fermentation remain on the surface of the grain, and may even persist throughout the entire process.
In wet processing, the group of lactic acid bacteria (such as Leuconostoc, Lactococcus, and Lactobacillus ) was most commonly identified, along with the Enterobacteria and yeasts ( Pichia and Starmerella ). Several metabolites involved in the activity of lactic acid bacteria, such as lactic acid, acetic acid, and mannitol, are produced in mucilage and are also found in coffee beans.
For dry processing, the occurrence of different types of fungi is more diverse than for wet processing, typically yeasts. Meanwhile, the bacterial group exhibited a diversity of acetic acid bacteria and lactic acid bacteria. The involvement of these microorganisms allows the accumulation of related metabolites such as gluconic acid and sugar alcohols in the pulp of the dried coffee cherries. Therefore, both wet and dry processing methods have significant involvement in the microbial community structure and the composition of the final green coffee bean.
As such, there is always a microbiome that lingers on green coffee beans and may even persist throughout the entire process, experts from SCA call this phenomenon the fermentation effect and it is the main driving force of the whole fermentation process.
Metabolism in coffee
On the other hand, the coffee bean is also a living entity, constantly interacting and reacting with its environment. Like any other living creature, the active metabolism of coffee beans will occur during processing.
The central location of the endosperm (coffee beans are always located in the center of the fruit and hold the endosperm inside) allows them to adapt to external environmental stressors.
With typical changes such as moisture and oxygen concentration, seeds will change their metabolic composition to suit survival (including the accumulation or utilization of carbohydrates, amino acids, and organic acids within the seed) or for germination.
These are the same factors that contribute to the difference between wet-processed and naturally-dried coffee.
Therefore, when we talk about the impact of coffee processing on taste, we are not just talking about the flavors created by the fermentation of coffee, we are also talking about the effects of coffee fermentation fundamental change due to the metabolic activity of the coffee bean itself.
In general, the flavor potential obtained from the fermentation of green coffee beans is closely related to the final cup quality. For example, Caffeine, CGA, and trigonelline are responsible for the bitter and astringent taste of coffee.
Since dry-processed green coffee beans contain many of these compounds, the bitterness of the extract will be higher than that of similar coffee in the wet process.
Different fermentations accumulate different flavor potentials
Under different processing conditions, both microbiology and local metabolism affect the flavor potential of the coffee beans and thus determine the final flavor quality.
The length of fermentation represents a potentially significant impact on coffee quality. While long fermentation is often thought to degrade the quality of the coffee, resulting in a pungent, foul, or sour taste, it can also have positive effects if the right controls are provided.
Under hygienic treatment conditions (especially for fermentation tanks and washing channels), longer fermentation allows more time for beneficial microorganisms to develop and results in more efficient fermentation.
The prolonged fermentation effect on green coffee beans may be reflected in a higher concentration of microbial metabolites (eg, lactic acid and mannitol) together with a higher content of organic compounds volatile like floral or fruity aromas. Modulation of the abundance of these flavor precursors on green coffee, indicating that longer fermentation leads to an intensification of fruity notes in the cup.
The impact of the microbiome
With mucilage (wet fermentation), sucrose is completely consumed at the end of fermentation, no matter how long it lasts. The decline in fructose and glucose concentrations was proportional to the fermentation time.
In turn, wet fermentation entails a significant accumulation of metabolites associated with microbial activity, including acetic acid, ethanol, glycerol, lactic acid, and mannitol. These compounds were accumulated in increasing concentrations with fermentation time.
Compared with mucilage, greater variation in metabolite concentrations occurs in coffee’s endosperm (also known as the seed embryo). After fermentation, the concentration of fructose, glucose, sucrose, and caffeine in the seeds decreased significantly.
The prolonged fermentation time decreased sucrose concentrations and increased concentrations of acetic acid, ethanol, glycerol, glucuronic acid, lactic acid, mannitol, and succinic acid. The accumulation of these compounds is proportional to the fermentation time.
In general, wet-processed green coffee beans contained higher concentrations of citric acid and erythritol while concentrations of fructose, glucose, caffeic acid, caffeine, trigonelline, and certain CQA isomers showed reduced expression.
Notes on dry processing
For the dry processing, obvious changes in metabolite concentrations occurred in the crust, whereas fewer changes were found in the endosperm. In general, sucrose will be depleted in the outer skin of the fruit during dry processing, in addition, the concentration of glucose and fructose will decrease.
Whereas the concentration of glycerol and mannitol will increase sharply. The concentration of organic acids, including lactic acid, gluconic acid, and glucuronic acid is almost doubled compared with wet processing.
During drying, if the granules are not spread (but piled up) stalled aeration will promote chlorogenic acid degradation (CGA) and caffeic acid generation by endogenous enzymes as well as volatiles slightly higher in endosperm than in wet-processed coffee beans.
High humidity will allow such yeasts to grow and increase the concentrations of the metabolites acetic acid, gluconic acid, ethanol, and glycerol in the pericarp and endosperm. All of these developments result in poor quality coffee that has a musty and earthy taste.
The downside of prolonged fermentation, however, is the exacerbation of the hypoxia in the endogenous metabolism of the grain, which affects the concentration of simple carbohydrates (e.g. glucose and fructose), acids, lipids, amino acids (eg, aspartic acid and alanine) and organic acids (eg, succinic acid).
These listed compounds can act as major precursors in a variety of chemical reactions during roasting, especially the Maillard reaction, and produce the characteristic coffee flavor.
When the beans are submerged in water, the low oxygen levels trigger the germination mechanism of the beans, leading to an anaerobic carbohydrate-consumption reaction, which is even more intense during prolonged fermentation.
Coffee beans will consume carbohydrate resources continuously through the breakdown of sugars. In addition, during the soaking process, the osmotic pressure facilitates the diffusion of monosaccharides and brings the microbial metabolites accumulated during fermentation into the seeds.
Therefore, the soaking process of coffee beans during wet fermentation not only facilitates the purification of these compounds but also affects the flavor quality of the coffee.
In addition, drying after fermentation induces a stress response due to dehydration and activates an aerobic metabolic mechanism in the endosperm. Overall, this process slows down the glucose and fructose consumption rate in the bean and contributes to the difference in concentrations of pre-flavor compounds in coffee (due to mass loss).
In summary, all processing steps contribute to the difference in concentrations of pre-flavor compounds in coffee. Therefore, based on the technological aspect (especially the time of fermentation, soaking, and drying) it is possible to determine the taste of the grain, because of the accumulation of microbial metabolites and the endogenous mobilization of the seeds. of the coffee, bean cell can change the overall composition of the coffee bean.
The role of coffee varieties in the fermentation process
Different coffee varieties will show different variations in the nutritional composition of the mucilage (and many other parts) in fresh coffee cherries. This is the main source of nutrients for microorganisms, so the difference in the composition of the mucilage between different coffee varieties also affects the extent of the fermentation effect.
For example, Typica berries from Latin America have a sweeter, more nutritious mesocarp layer than those from Catimor in Asia.
Combined with extrinsic factors, such as ambient temperature, studies from SCA show that this affects the pH profile, dynamics of the fermenter microbiota, and the conversion components chemical during fermentation.
Therefore, it is important to take the coffee variety into account when assessing the potential impact of processing practices.
- The Fermentation Effect – 25 Magazine, Issue 10 | www.scanews.coffee
- Relevant research papers have been published in: De Bruyn, F ., Zhang, SJ , Pothakos, V.*, Torres, J., Lambot, C., Moroni, AV, De Vuyst, L. (2017). Exploring the impacts of post-harvest processing on the microbiota and metabolite profiles during green coffee bean production.